Examples with MassList net.sf.mzmine.datamodel.MassList used on opensource projects

Example 31 with MassList

use of net.sf.mzmine.datamodel.MassList in project mzmine2 by mzmine.

the class IsotopePeakScannerTask method checkParameters.

private boolean checkParameters() {
    if (charge == 0) {
        setErrorMessage("Error: charge may not be 0!");
        setStatus(TaskStatus.ERROR);
        return false;
    }
    if (!FormulaUtils.checkMolecularFormula(element)) {
        setErrorMessage("Error: Invalid formula!");
        setStatus(TaskStatus.ERROR);
        return false;
    }
    if (accurateAvgIntensity || ratingType == RatingType.TEMPAVG) {
        if (massListName.equals("") && ratingType == RatingType.TEMPAVG) {
            setErrorMessage("Error: Rating Type = temporary average but no masslist was selected.\nYou can" + " select a mass list without checking accurate average.");
            setStatus(TaskStatus.ERROR);
            return false;
        }
        if (peakList.getNumberOfRawDataFiles() > 1) {
            setErrorMessage("The number of raw data files of feature list \"" + peakList.getName() + "\" is greater than 1. This is not supported by this module.");
            setStatus(TaskStatus.ERROR);
            return false;
        }
        RawDataFile[] raws = peakList.getRawDataFiles();
        boolean foundMassList = false;
        for (RawDataFile raw : raws) {
            int[] scanNumbers = raw.getScanNumbers();
            for (int scan : scanNumbers) {
                MassList[] massLists = raw.getScan(scan).getMassLists();
                for (MassList list : massLists) {
                    if (list.getName().equals(massListName))
                        foundMassList = true;
                }
            }
        }
        if (foundMassList == false) {
            setErrorMessage("Feature list \"" + peakList.getName() + "\" does not contain a mass list by the name of " + massListName + ".");
            setStatus(TaskStatus.ERROR);
            return false;
        }
    }
    return true;
}

Example 32 with MassList

use of net.sf.mzmine.datamodel.MassList in project mzmine2 by mzmine.

the class ScanSelectPanel method getFilteredDataPoints.

/**
 * Remaining data points after filtering
 *
 * @return
 */
@Nullable
public DataPoint[] getFilteredDataPoints() {
    if (scans != null && !scans.isEmpty()) {
        Scan scan = scans.get(selectedScanI);
        MassList massList = ScanUtils.getMassListOrFirst(scan, massListName);
        if (massList != null)
            return ScanUtils.getFiltered(massList.getDataPoints(), noiseLevel);
    }
    return null;
}

Example 33 with MassList

use of net.sf.mzmine.datamodel.MassList in project mzmine2 by mzmine.

the class ScanSelectPanel method analyzeScan.

private void analyzeScan(Scan scan) {
    MassList massList = ScanUtils.getMassListOrFirst(scan, massListName);
    if (massList != null) {
        DataPoint[] dp = massList.getDataPoints();
        double tic = ScanUtils.getTIC(dp, noiseLevel);
        int signals = ScanUtils.getNumberOfSignals(dp, noiseLevel);
        lbTIC.setText(MZmineCore.getConfiguration().getIntensityFormat().format(tic));
        lbSignals.setText("" + signals);
        lbTIC.getParent().revalidate();
        lbTIC.getParent().repaint();
    }
}

Example 34 with MassList

use of net.sf.mzmine.datamodel.MassList in project mzmine2 by mzmine.

the class ExtractScansTask method exportScans.

private void exportScans(File dir, RawDataFile raw, int start, int scans, double pp) {
    // Open file
    DecimalFormat format = new DecimalFormat("00");
    File fileDir = new File(dir, FileAndPathUtil.eraseFormat(raw.getName()));
    FileAndPathUtil.createDirectory(fileDir);
    int end = Math.min(scans + start, raw.getNumOfScans());
    String linescans = "scan" + delimiter + raw.getScanNumbers()[start] + delimiter + "to" + delimiter + raw.getScanNumbers()[end - 1] + "\n";
    String lineRT = "RT" + delimiter + raw.getScan(raw.getScanNumbers()[start]).getRetentionTime() + "to" + raw.getScan(raw.getScanNumbers()[end - 1]).getRetentionTime() + "\n";
    String linePath = raw.getName() + "\n";
    String lineOptions = "export of" + delimiter;
    if (!useCenterTime) {
        double st = raw.getScan(raw.getScanNumbers()[start]).getRetentionTime();
        double et = raw.getScan(raw.getScanNumbers()[end]).getRetentionTime();
        lineOptions += scans + delimiter + "scans from time " + delimiter + st + " to " + et + "\n";
    } else if (autoMax) {
        lineOptions += scans + delimiter + "scans around scan with maximum intensity:" + delimiter + raw.getScanNumbers()[scanMaxTIC] + "\n";
    } else {
        lineOptions += scans + delimiter + "scans around center time:" + delimiter + centerTime + "\n";
    }
    for (int i = start; i < end; i++) {
        FileWriter writer;
        File file = new File(fileDir, "scan" + format.format((i - start + 1)) + ".csv");
        StringBuilder out = new StringBuilder();
        try {
            writer = new FileWriter(file);
        } catch (Exception e) {
            e.printStackTrace();
            return;
        }
        // EXPORT
        try {
            Scan s = raw.getScan(raw.getScanNumbers()[i]);
            // write header
            if (exportHeader) {
                out.append(linePath);
                out.append(linescans);
                out.append(lineRT);
                out.append(lineOptions);
                out.append("TIC" + delimiter + s.getTIC() + "\n");
                out.append("scan number" + delimiter + raw.getScanNumbers()[i] + "\n");
                out.append("retention time" + delimiter + s.getRetentionTime() + "\n\n");
                out.append("mz" + delimiter + "intensity\n");
            }
            // write data
            if (useMassList) {
                MassList mass = s.getMassList(massList);
                DataPoint[] dp = mass.getDataPoints();
                for (int k = 0; k < dp.length; k++) {
                    out.append(dp[k].getMZ() + delimiter + dp[k].getIntensity() + "\n");
                }
            } else {
                for (int k = 0; k < s.getNumberOfDataPoints(); k++) {
                    DataPoint dp = s.getDataPoints()[k];
                    out.append(dp.getMZ() + delimiter + dp.getIntensity() + "\n");
                }
            }
            writeBuffered(writer, out.toString(), 8192);
        } catch (IOException e1) {
            e1.printStackTrace();
        } finally {
            // Close file
            try {
                writer.close();
            } catch (Exception e) {
                e.printStackTrace();
                return;
            }
        }
        // 
        perc += pp / (double) scans;
    }
}

Example 35 with MassList

use of net.sf.mzmine.datamodel.MassList in project mzmine2 by mzmine.

the class ExportScansTask method exportText.

/**
 * Export the chromatogram - text formats
 *
 * @throws IOException if there are i/o problems.
 */
public void exportText() throws IOException {
    // Open the writer - append data if file already exists
    final BufferedWriter writer = new BufferedWriter(new FileWriter(exportFile, true));
    try {
        for (Scan scan : scans) {
            LOG.info("Exporting scan #" + scan.getScanNumber() + " of raw file: " + scan.getDataFile().getName());
            // Write Header row
            switch(extension) {
                case "txt":
                    writer.write("Name: Scan#: " + scan.getScanNumber() + ", RT: " + scan.getRetentionTime() + " min");
                    writer.newLine();
                    break;
                case "mgf":
                    writer.write("BEGIN IONS");
                    writer.newLine();
                    writer.write("PEPMASS=" + scan.getPrecursorMZ());
                    writer.newLine();
                    writer.write("CHARGE=" + scan.getPrecursorCharge());
                    writer.newLine();
                    writer.write("MSLEVEL=" + scan.getMSLevel());
                    writer.newLine();
                    writer.write("Title: Scan#: " + scan.getScanNumber() + ", RT: " + scan.getRetentionTime() + " min");
                    writer.newLine();
                    break;
                case "msp":
                    break;
            }
            // Write the data points
            DataPoint[] dataPoints = null;
            if (useMassList && massListName != null) {
                MassList list = scan.getMassList(massListName);
                if (list != null)
                    dataPoints = list.getDataPoints();
            }
            if (dataPoints == null)
                dataPoints = scan.getDataPoints();
            final int itemCount = dataPoints.length;
            progressMax = itemCount;
            for (int i = 0; i < itemCount; i++) {
                // Write data point row
                writer.write(dataPoints[i].getMZ() + " " + dataPoints[i].getIntensity());
                writer.newLine();
                progress = i + 1;
            }
            // Write footer row
            if (extension.equals("mgf")) {
                writer.write("END IONS");
                writer.newLine();
            }
            writer.newLine();
        }
    } catch (Exception e) {
        throw (new IOException(e));
    } finally {
        // Close
        writer.close();
    }
}